kilkul b'shir and the ideal of a makom mikdash

The Mishna in R"H tells us that one time the witnesses who saw the new moon came late in the day, after the usual time at which the afternoon korban tamid was offered, and this led to niskalkilu haLevi'im b'shir, there was some confusion in the Beis haMikdash as to what to do -- the gemara discusses whether the shira accompanying the korban was omitted, or the wrong shirah was recited -- whatever happened, something was wrong. In response to this event a takana was made that if the witnesses arrive too late, even though their testimony would mean that the day should be declared the beginning of a new month and year, we do not accept their late testimony and instead hold the witnesses over and declare the new year as starting from the next day.

Over Yom Tov I heard an insightful comment in the name of R' Chait, the R"Y of Yeshiva Bnei Torah. R' Chait explained that it was davka because this kilkul, this confusion ,took place in the Mikdash itself, that caused the need for a legislative intervention and creation of takanos. The Mikdash is supposed to inspire all who enter within its walls and serve as a model of holiness and an example of the Torah ideal. For confusion and halachic uncertainty to exist in the very place we hold up as a model of perfection is intolerable. If our model of perfection has such flaws, what impression does that give of the Torah system as a whole? Therefore, the situation demanded remediation.

There is a natural mussar haskel from here (which I did not hear b'shem R' Chait, but I will say it anyway): in each of our little mikdash me'ats that we learn in and daven in every day, in our shuls and shteibelach and batei medrash, what takanos do we need to put in place to insure that these oases are models of perfection? What do we need to do to insure that someone who steps into a makom Torah feels insipred, feels drawn to Torah and its beauty, and does not witness kilkul b'shir?